Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels

BMC Bioinformatics. 2019 Dec 23;20(Suppl 21):707. doi: 10.1186/s12859-019-3195-5.


Background: Use of medication can cause adverse drug reactions (ADRs), unwanted or unexpected events, which are a major safety concern. Drug labels, or prescribing information or package inserts, describe ADRs. Therefore, systematically identifying ADR information from drug labels is critical in multiple aspects; however, this task is challenging due to the nature of the natural language of drug labels.

Results: In this paper, we present a machine learning- and rule-based system for the identification of ADR entity mentions in the text of drug labels and their normalization through the Medical Dictionary for Regulatory Activities (MedDRA) dictionary. The machine learning approach is based on a recently proposed deep learning architecture, which integrates bi-directional Long Short-Term Memory (Bi-LSTM), Convolutional Neural Network (CNN), and Conditional Random Fields (CRF) for entity recognition. The rule-based approach, used for normalizing the identified ADR mentions to MedDRA terms, is based on an extension of our in-house text-mining system, SciMiner. We evaluated our system on the Text Analysis Conference (TAC) Adverse Drug Reaction 2017 challenge test data set, consisting of 200 manually curated US FDA drug labels. Our ML-based system achieved 77.0% F1 score on the task of ADR mention recognition and 82.6% micro-averaged F1 score on the task of ADR normalization, while rule-based system achieved 67.4 and 77.6% F1 scores, respectively.

Conclusion: Our study demonstrates that a system composed of a deep learning architecture for entity recognition and a rule-based model for entity normalization is a promising approach for ADR extraction from drug labels.

Keywords: Adverse drug reaction; Deep learning; Entity normalization; Entity recognition; Machine learning; Text mining.

MeSH terms

  • Data Mining
  • Deep Learning
  • Drug Labeling*
  • Drug-Related Side Effects and Adverse Reactions*
  • Machine Learning*
  • Neural Networks, Computer
  • United States
  • United States Food and Drug Administration